Prediction of Inter-residue Contact Clusters from Hydrophobic Cores

Abstract

A contact map is a key factor representing a specific protein structure. To simplify the protein contact map prediction, we predict the inter-residue contact clusters centered at the groups of their surrounding inter-residue contacts. In this paper, we adopt a Support Vector Machine (SVM)-based approach to predict the inter-residue contact cluster centers. The input of the SVM predictor includes sequence profile, evolutionary rate and predicted secondary structure. The SVM predictor is based on hydrophobic cores that may be considered as locations of the inter-residue contact clusters. About 35% of clustering centers of inter-residue contacts can be predicted accurately.